If a study factor includes multiple quantification channels, the application calculates the p-value for ratios that use those study factors the same way that it calculates the p-value for a non-nested biological replicate design (see Create non-nested designs). The advantage of this type of calculation is that it does not require you to create study factors.
When you do not use study factors, the resulting Generated Sample Groups pane and the Generated Ratios pane on the Grouping & Quantification page resemble the panes in the following figure.
When you use the ANOVA (Individual Proteins) p-value calculation method, to ensure that the application calculates p-values for ratios that include those study factors, you must group quantification channels underneath a study factor. In this example, the green boxes show study factors 5, 7, 9, and so forth.
